Nomenclature of Antimicrobial Peptides
The nomenclature of AMPs has not been standardized and many methods are in use. However, there are three major methods to name a newly discovered antimicrobial peptide.
1. Peptide property-based
LL-37: a 37-residue human host defense peptide starting with a pair of leucines (LL);
PR-39: a 39-residue AMP rich in Pro and Arg residues;
Cathelicidins: coined from the highly conserved "cathelin" domain of the precursur proteins by Zanetti. Initially this name refers to the precursor protein and now it is widely accepted as the name for a family of AMPs whose precursor proteins share the "cathelin" domain;
Defensins: related to the peptide function as a defense molecule (coined by Lehrer's group).
2. Peptide source-based
Termicin: an AMP from termites (common name);
LEAP-2: liver expressed antimicrobial peptide 2;
Palicourein: derived from Palicourea condensata (scientific name);
3. Peptide property and source-combined
Ee-CBP: derived from Euonymus europaeus Chitin Binding Protein or peptide;
So-D1: derived from Spinacia oleracea Defensin 1;
Ct-AMP1: derived from Clitoria ternatea antimicrobial peptide 1.
4. Peptide discovery method-based
DFTamP1: database filtering tech designed antimicrobial peptide 1;
Combi-2: combinatorial library identified antimicrobial peptide 2;
GLK-19: peptide amino acid composition and length;
Avoid using the following database search terms when naming your peptides:
Examples are XX, BB, ZZ, and JJ, predicted, synthetic, bacteria, plants, fungii, animals, reptiles, amphibians, frogs, fish, worms, birds, etc. It is not good idea to report your AMPs as peptide 1 to n, either.
Major Reference: Wang G. (editor) Antimicrobial Peptides: Discovery, Design and Novel Therapeutic Strategies, CABI, England, 2010.